These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anvilicious: Alright, Mr. Leterrier, we get it. Men don't need gods. Is it really necessary to remind us of that every ten minutes though? On the other hand, perhaps its just a bad case of the studio thinking Viewers Are Morons.
Big Lipped Alligator Moment: If you've never seen the original you might be asking yourself what a futuristic robotic owl is doing laying in the bottom of a trunk in ancient Greece.
Actually Older than You Think: the futuristic robotic owl is actually mentioned in Greek myths (I don't recall if it is in the myth of Perseus or others) as a creation of Hephaestus gifted to Athena. And if you think the greeks where ahead of their time with the robo-owl wait till you find out about the two female assistants Hephaestus made for himself, out of chromed steel.
The conversation that young Perseus has with Spyros about his anxieties regarding the new baby and Spyros not being his biological father. It has no bearing on the plot except to set up a character who is killed a few scenes later without so much as a single line. You really have to wonder why they bothered with either one.
In the sequel, when Perseus, Andromeda, and Aginor enter Tartarus, Andromeda thinks she sees Korrina, the soldier who prayed to Ares, walking around, while Perseus appears to see his son, Helius. Unless I'm missing something here, what was that all about?
Hallucinations - Hephaestus mentioned the greatest traps were mental and not physical.
The minotaur as well. It turns up, gets killed and is never mentioned again.
Critical Research Failure: The Chimera has wings, which would have been cool but misses out one important bit of the myth: the reason Bellerophon had to go through all the trouble of capturing Pegasus so he can fly above the monster, safe from its flames and fangs. This would, quite logically, not work if the Chimera could fly.
Well, maybe Pegasus could fly faster and/or higher than the Chimera. It still counting. And don't forget, it would make the battle more exciting.
Designated Villain: Medusa again, with a deeply tragic backstory. Io even seems to think she deserves pity. Of course, she's more of a means to end to defeat the real villain, but still.
Strangled by the Red String: The alternate ending from the Blu-Ray is closer to the original in that Perseus and Andromeda fall in love... even though they barely share screentime together due to Andromeda being Demoted to Extra, Perseus is a Darker and Edgier hero than the "motivated by love" original, and the rest of the movie builds up a different love interest in Io.
This is due to Executive Meddling. The original cut of the film had more development in Perseus and Andromeda's romance with Io and Perseus being Like Brother and Sister. Perseus's original motivation to save Andromeda was more to make a point that nobody should have to die for the Gods that was edited to being about getting to Hades instead. The studio had several scenes reshot to add in romantic moments between Perseus and Io as well as cutting down Andromeda's screen time. Andromeda's first scene does show some of the hints of the original romance, from her interaction with Perseus.
They Wasted a Perfectly Good Plot: There were times when it felt it they were setting up to deliver the message "just because they're your children/you created them doesn't justify abusing them," but it never happened.
What an Idiot: And to think...if Hades hadn't gone out of his way to be a dick by killing Perseus's family, he would have been able to pull of his plan to seize power without a hitch.
If the Harpy that stole the bag with Medusa's head in it had say, dropped it in the sea, or fed it to the Kraken, Hades would have won straight off.
They could have turned right around and, you know, used it on Perseus. Just saying.
Feeding it to the Kraken is not a good idea. It would have petrified the monster from the inside out when his gastric fluids dissolved the bag.
Only if the Kraken had eyes inside its stomach. You need to look at Medusa's head for it to work.
If Perseus had just gone with Zeus when he asked him to in the sequel, he probably could have stopped Ares and Hades from imprisoning Zeus in the first place. What's worse is that he makes a big deal out of not leaving his son's side...and then five minutes later, leaves his son's side and a Chimera attacks his village, nearly killing the both of them. Brilliant, Perseus. Brilliant.
Visual Effects of Awesome: Painfully averted with the slapped on 3D, but the Kraken looked freaking awesome. It's a shame he was only there for less than five minutes. For those watching the film in 2D however, the CGI is exceptional.
The sequel's special effects are spectacular, most notably Kronos, who's essentially a walking volcano of death and destruction. He's truly a sight to behold.